GLOSSARY

ABC transport (ATP-binding cassette transport)  A form of active transport bringing solutes into the cell facilitated by solute- specific binding proteins that convey the solute to the membrane and  there trigger pore opening by ATP hydrolysis.

Acetogenic  bacteria  Anaerobic  bacteria  that synthesize acetic acid from CO2 and secrete the acetic acid into the medium.

Acidophile  Organism that grows between pH 1 and 4 and not at neutral pH.

Actinobacteria  A phylum and a class of Gram- positive bacteria with high guanine- cytosine (GC) content that includes the genus Streptomyces, soil bacteria that produce secondary metabolites of medical and industrial importance.

Active transport  The movement of solutes across a membrane against a concentration gradient powered by cellular energy.

Acyl carrier proteins  Cytoplasmic proteins that facilitate phospholipid synthesis by preventing aggregation of the hydrophobic fatty acids and ferrying them to the waiting polar head group. 

Aerobic respiration  A process by which electrons,  either alone or as hydrogen atoms, are passed from an electron donor to oxygen (terminal electron acceptor) while simultaneously generating a transmembrane proton  gradient.

Aerotolerant  anaerobe  Organism  that  cannot use  oxygen  as  an  electron  acceptor  during respiration but can grow in its presence.

Akinete  A thick- walled, dormant bacterial cell derived from a vegetative cell and capable of reversion to its previous form, produced in response to adverse conditions by some cyanobacteria and other bacteria.

Allosteric protein  A protein whose conformation and catalytic function are modulated by the binding of a specific molecule to a binding site distinct from the catalytically active site.

Amphibolic pathway A pathway in which both anabolism and catabolism could occur together. e.g. during operation of TCA cycle,  Acetyl CoA the product of the betaoxidation of fatty acids is further metabolized (catabolism) at the same time intermediates of this pathway like oxaloacetate is used for synthesis of aminoacids like aspartate and methionine (anabolism).

Anaerobe  Organism that does not use oxygen as an electron acceptor during respiration.

Anaerobic respiration  A process in which electrons,  either alone or as hydrogen atoms, are passed from an electron donor to a terminal electron acceptor (an organic  or inorganic molecule other than oxygen e.g. NO3, SO4, fumarate) while simultaneously generating a transmembrane proton gradient, leading to ATP synthesis.

Anaplerotic reactions - biochemical reactions that replenish the intermediates (that are removed for other biosynthetic reactions e.g. oxaloacetate of TCA cycle removed for biosynthesis of methionine and aspartate) of a metabolic pathway. e.g. pyruvate carboxylase and pyruvate dehydrogenase that supplies oxaloacetate from pyruvate.

Anoxygenic photosynthesis  A process in which light energy is harnessed to generate ATP and reducing power while simultaneously oxidizing inorganic  molecules (other than  water) or organic compounds.

Alkaliphile (alkalophile)  Organism that grows at  pH  above  9,  often  with  an  optimum between 10 and 12.

Archaellum  The archaeal functional equivalent of the bacterial flagellum

Assimilation  The incorporation of an environmental element, such as phosphorus, into precursor metabolites.

ATP synthase An enzyme complex embedded in the cell membrane that uses the proton motive force to drive the phosphorylation of ADP to form ATP.

Autotroph  An organism that can use an inorganic carbon molecule (especially CO2) such as carbon dioxide as its sole carbon source.

Auxotroph  An organism that, due to a mutation, has lost the ability to synthesize a particular metabolite or nutrient; alternatively, an organism that requires an external source of one or more building blocks.

Axial filament  During endospore differentiation, the elongated form of the nucleoid.

Bacteriochlorophyll  A class of photosynthetic pigments found in Bacteria, members of which vary in their ability to harvest light of different wavelengths.

Bacteriocin  Any of several classes of peptides that are produced and released by Bacteria and Archaea, which kill or inhibit the growth of members of the same or closely related species by a variety of tactics.

Bacteriocyte  specialized cells of some insects that harbor large numbers of endosymbiotic bacteria.

Bacteriorhodopsin  A membrane protein in some haloarchaea that uses energy from sunlight to pump protons out of the cell, thus creating a proton motive force to drive the production of ATP.

Bacteroid  A differentiated bacterial cell in a root nodule that carries out nitrogen fixation .

Balanced growth  A growth state characterized by (1) exponential growth, (2) a constant mean cell size, and (3) the same proportional increase of all cell constituents over any given interval of time.

Barophile  An organism that grows optimally at pressures exceeding 1 atm (see piezophile).Binary cell division (binary fission)  A common mechanism whereby cells approximately double in size and then divide to produce two equal  daughter cells.

Biofilm   A community of microbes that adhere to each other and to a surface, are typically embedded in a secreted matrix, practice division- of- labor, and often adopt a characteristic architecture.

Biogeochemical cycles  The complex interconversions of bioelements (carbon, oxygen, nitrogen, sulfur, and phosphorus) that balance utilization with replenishment to maintain relatively stable global levels.

Bioluminescence  The production and emission of light by some bacteria and other organisms.

Bt toxin  Any member of a group of proteins with insecticidal properties made by Bacillus thuringiensis during sporulation.

Budding  Asymmetrical cell division found in some yeasts in which a small  daughter cell forms as a protuberance (a “bud”) from the  mother cell.

Building blocks  Molecules that are synthesized from precursor metabolites and then polymerized to build cellular macromolecules. Example: amino acids are the building blocks of proteins.

Capsule  A diffuse layer of exopolysaccharide or polypeptide surrounding, and attached to, the cell envelope of some Bacteria.

Carboxysome  Intracellular compartments in Bacteria that are bounded by a protein shell and that contain the enzymes required to fix carbon dioxide, including RuBisCO.

Candidatus bacteria Refers to group of bacteria that are non culturable in laboratory conditions, but well studied by 16S rRNA gene sequencing and genomic studies, meaning well studied but not available in pure culture. e.g. "Candidatus Brocardia anammoxidans" involved in the anaerobic ammonia oxidation in waste water treatment plants. 

Note: here the term candidatus need to be underlined or typed in italic with first letter in Capital, the genus and species name should NOT be underlined and should be non italic; all the words need to be placed within inverted commas ("Xxx  xxx"). 

Cell envelope  In Bacteria and Archaea, all the layers that bound the cell including the cell membrane and surrounding structures such as cell wall, outer membrane, and S- layer.

Cell wall  A rigid layer made of a polymer of sugars and amino acids that surrounds the cell membrane of most Bacteria and some Archaea and provides structural support.

Chaperone  proteins A kind of Proteins  that  transiently bind to other proteins and assist in proper folding of the target protein and/or transport to a correct cellular site.

Chaperonins  Multisubunit complexes of chaperone proteins.

Chemiosmosis  The movement of ions across a biological membrane down a concentration gradient, such as the movement of protons used by cells to create ATP.

Chemoautotroph  An organism that gains energy for growth from the oxidation of chemicals (organic or inorganic molecules) and carbon from an inorganic carbon molecule (such as carbon dioxide).

Chemoheterotroph  An organism that gains energy for growth from the oxidation of chemicals (organic or inorganic molecules) and carbon from an organic carbon source.

Chemiosmosis  The movement of ions across a biological membrane down a concentration gradient, such as the movement of protons used by cells to create ATP.

Chemoautotroph  An organism that gains energy for growth from the oxidation of chemicals (organic or inorganic molecules) and carbon from an inorganic carbon molecule (such as carbon dioxide).

Chemoheterotroph  An organism that gains energy for growth from the oxidation of chemicals (organic or inorganic molecules) and carbon from an organic carbon source.

Chemotroph  An organism that obtains its energy from oxidation of organic or inorganic molecules.

Chlorophyll  A class of photosynthetic pigments found in numerous bacterial phyla as well as in chloroplasts.

Comammox  Complete ammonia oxidation to nitrate via nitrite by a single microbe.

Commensal  An organism that lives in association with and benefits from another organism without affecting (neither harming nor benefiting) that partner.

Crystalline surface layer (S- layer)  The outermost layer of the cell envelope of some Bacteria and Archaea composed of a regular lattice of a single protein or glycoprotein.

Culture- independent method  Or cultivation - independent method, any method that assesses the composition and properties (e.g., relative abundance of taxa, genes, or proteins expressed) of microbial communities in an environment without requiring culturing of the microbes.

Cyanobacteria  A bacterial phylum whose members contain chlorophyll a and carry out oxygenic photosynthesis.

Cyclic photosynthesis  Photosynthesis in which the terminal electron acceptor is the same chlorophyll that was light excited and donated the electron at the start of the electron transport chain.

Cytoplasm  The fluid material enclosed by the cell membrane.

Cytosol  The liquid portion of the cytoplasm.

Dalton (Da)  All atomic and molecular weights refer to the carbon isotope,  12 C, which is 12 Da or 1.661 × 10−24  g. Daltons are numerically equal to molecular weights and can be used as units when molecular weight units 

Dehydrogenase  They are  enzymes that catalyze oxidation–reduction reactions in which hydrogens as well as electrons are transferred. They are named after one of the substrates (e.g., pyruvate dehydrogenase).

Denitrification   The microbial conversion of nitrate to dinitrogen.

Diauxic growth  Microbial growth characterized by two phases with different growth rates. e.g. growth with glucose and sucrose.

Dimethyl sulfide   A volatile sulfur compound, produced abundantly by marine bacteria, that escapes into the atmosphere where it nucleates cloud formation.

Dipicolinic acid  (DPA) A low- molecular- weight compound accumulated in the forespore during endospore differentiation, where it dehydrates the endospore and protects the DNA from heat denaturation.

Dissimilation  The microbial use of a molecule, such as nitrate and sulfate, as an energy source.

Electrode potential  The tendency of a molecule to accept an electron from another molecule is given by its electrode potential, E, also called the reduction potential, the redox potential, or the oxidation–reduction potential.

Electron transport chain  A series of membrane proteins with different redox potentials that move electrons sequentially from an electron donor to a terminal electron acceptor down an energy gradient while simultaneously exporting protons across the membrane to generate the proton motive force used to generate ATP.

Endergonic reaction  A nonspontaneous chemical reaction that requires an energy input to proceed (the change in Gibbs  free energy is positive).

Energy charge  A ratio representing the relative amounts of ATP, ADP, and AMP in a cell, thus a mea sure of the cell’s energy  status.

Energy- coupled transport  Transport of specific molecules across the outer  membrane of Gram- negative bacteria against a concentration gradient.

Enterochelin  A siderophore made by E. coli to import iron into the cell.

Enterosome  Intracellular compartments of enteric bacteria that are bounded by a protein shell and contain the enzymes required to metabolize specific compounds such as 1,2- propanediol and ethanolamine.

Envelope  The lipid- carbohydrate- protein membrane surrounding the capsid of some viruses.

Environmental stress  Any significant change in a microbe’s environment, e.g., a shift in temperature, pH, nutrient availability.

Enzymes  Molecules (proteins or RNAs) that catalyze chemical reactions.

Epibiont  An organism that lives on the surface of a host organism, typically without harm to the host.

Exopolysaccharide (EPS)  Polysaccharides secreted outside the cell that form a protective capsule or slime layer.

Exospore  A spore produced by some filamentous bacteria by pinching off the tips of the filamentous cells.

Exponential phase  A bacterial growth phase characterized by balanced growth in which a constant rate of growth and cell division produces an exponential increase in the number of cells.

Extremophile  An organism that thrives in and may require what, from the anthropocentric point of view, is an inhospitable or “extreme” environment.

Facilitated diffusion  selective passive transport of molecules across a membrane that is aided by specific interactions with membrane proteins.

Facultative aerobe  An organism that can grow in the presence or the absence of oxygen.

Facultative  anaerobes  Organisms  that  can grow anaerobically in the absence of oxygen or will grow by respiration if oxygen is available.

Facultative  autotroph  Organisms  that  can grow  on  CO2  as  sole  or  major  source  of carbon or on organic carbon.

Feedback inhibition  Negative regulation of the first enzyme in a biosynthetic pathway by the end product of the pathway acting as a negative allosteric effector.

Fermentation  A metabolic process that recycles NADH generated in fueling reactions to reduce pyruvate and other compounds derived from it, thereby converting organic substrates into acids, alcohols,  etc.

Fimbria (plural, fimbriae)  See pilus.

Flagellin  The peptide subunit that self- assembles to form flagellar filaments.

Flagellum (plural, flagella)  Cellular appendage of Bacteria composed of a  filament  anchored by a complex structure in the cell membrane that, fueled by ATP, rotates propeller- like to propel the cell.

Forespore  During endospore differentiation, the smaller  daughter cell following cell division that  will give rise to the endospore.

FtsZ  A prokaryotic protein, filamentous temperature sensitive protein Z, that assembles during cell division to form the Z- ring at the site of the  future septum.

Fueling reactions  The metabolic reactions that provide the precursor metabolites, energy, and reducing power required for growth and maintenance.

Generation time (g)  The time required for a population of cells to double in number.

Gliding motility  several types of nonflagellar bacterial motility produced by groups or individual cells.

Gluconeogenesis  A metabolic pathway that makes hexoses, such as glucose, from one- , two- , three- , or four- carbon substrates.

Glycolysis  A fueling pathway in which glucose is converted into two molecules of the precursor metabolite pyruvate, while also generating energy (ATP), reducing power (NADH), and precursor metabolites needed to synthesize sugars, amino acids, and fatty acids

Green bacteria  A group of anoxygenic phototrophs that contain chlorophyll pigments.

Great plate count anomaly A phrase that describes the observation that microscopic cell counts are significantly higher than corresponding counts of colony forming units. 

Growth rate is referred to the increase in the number or cell mass per unit time. 

Group translocation  A type of active transport that brings sugars into some bacteria using the phosphate group from phosphoenolpyruvate to phosphorylate the imported sugar and thereby render the sugar unable to penetrate the membrane to escape from the cell.

Growth metabolism  Metabolic reactions that directly contribute to the production of new cells.

Growth  yield  constant,  Y  The  amount  of  dry weight of cells produced per weight of nutrient used.

Halophile  Organism  that  requires  high  salt concentrations for growth.

Heat-shock  proteins  Proteins  that  transiently increase  in  amount  relative  to  most  cell proteins when the temperature is elevated. Several are chaperone proteins.

Heterocyst  A terminally differentiated cell pres ent in some filamentous cyanobacteria that is specialized for nitrogen fixation .

Heterotroph  Organism that uses organic carbon as a major source of carbon.

Homolactic fermentation  An auxiliary fueling fermentation that reduces pyruvate to lactate to recycle NADH.

Hydrogenosome  A membrane- bounded organelle found in some protists and fungi that was derived from mitochondria and that now generates ATP and produces hydrogen as a by- product.

Hyperthermophile  An organism that thrives in extremely hot environments and that typically grows optimally above 80°C.

Inclusion  A general term for internal structures in some prokaryotes that includes enterosomes, carboxysomes, magnetosomes, and gas vesicles, among  others.

Ion-coupled transport  The active transport of solutes across a membrane driven by the preexisting electrochemical gradient across that membrane.

Isoprenoid  A class of long-chain hydrocarbons found in archaeal membranes, where they take the place of the fatty acids found in bacterial membranes

Isomerase  Enzymes  that  catalyze  the  transfer of chemical groups (e.g., hydrogen or phosphate) within molecules to produce isomeric forms of a molecule with the same chemical formula.  For  example,  glucose  (C6H12O6) and fructose (C6H12O6) are isomers of each other because they have the same chemical formula, although their chemical structures are different.

Lag phase  When stationary-phase cells are provided adequate nutrients, the period of time before the cells resume growth.

Leghemoglobin  A form of plant hemoglobin found in root nodules that binds oxygen to protect the bacteroid nitrogenase.

Lithotroph  Organism  that  oxidizes  inorganic compounds as a source of energy for growth.

Magnetosome  A specialized, membrane- bounded intracellular structure of some bacteria that contains iron crystals that function as magnets used to orient the cell relative to the Earth’s magnetic field.

Maintenance metabolism  Metabolic reactions that do not directly contribute to the production of new cells, but rather maintain cellular functions.

Malolactic fermentation  In wine making, the bacterial conversion of the tart- tasting malic acid present in grapes to the milder lactic acid.

Mesophile  Organism  whose  growth  temperature optimum is between 25 and 40 °C.

Metagenome  All the DNA sequences retrieved from an environmental sample, which in complex communities typically represents only the more abundant community members.

Metagenomics  A culture- independent method in which DNA is extracted from an environmental sample and then sequenced without relying on primer- based amplification or cloning.

Methanogen  An archaeon that produces methane as a metabolic by-product.

Methylotroph  An organism that uses reduced one- carbon compounds, such as methane, as their carbon  source.

Microaerophile  An organism that requires oxygen but cannot tolerate high oxygen concentrations.

Microbiome  All the microbes that inhabit a par tic u lar environment, such as the human body, or all of the genetic information that they contain.

Mitosome  A membrane- bounded organelle of some parasitic protists living  under anaerobic or microaerophilic conditions, thought to be derived from mitochondria although they no longer produce ATP.

Midpoint potential (Em)  The electrode potential when the molecule is 50% oxidized.

Mutases  A  subclass  of  isomerases;  enzymes that transfer a functional group (e.g., a phosphate group) from one part of a molecule to another.

Murein  The type of peptidoglycan that forms bacterial cell walls.

Mycolic acid  A wax found in the membrane of tubercle bacilli that contains long, branched fatty acids.

Mycoplasma  Bacteria that lack a cell wall and, in many instances, incorporate sterols in their membrane for strength and rigidity.

Nitrification   The microbial oxidation of ammonia to nitrate carried out in two steps (ammonia to nitrite, then nitrite to nitrate) by two different organisms

Neutrophile  Organism that grows at a pH optimum near neutrality.

Obligate anaerobes  Organisms that will grow only  in  the  absence  of  oxygen  but  are  not necessarily killed by oxygen

Oligopeptide  Refers to a molecule of a few amino acids joined together by peptide bonds. Also referred to as a peptide. A  pentapeptide is an example of an oligopeptide. When many amino acids are joined together, the molecule is referred to as a polypeptide (MW < 10,000)or a protein (MW > 10,000).

Oxidative phosphorylation  In chemotrophs, the phosphorylation of ADP to generate ATP using the oxidation of chemical substrates as the energy source. 

Oxygenic photosynthesis  A process in which captured light energy is used to generate ATP and reducing power, with  water being oxidized in the process to produce O2 .

Pentose phosphate pathway  A fueling pathway that converts glucose into 5- carbon and 4- carbon precursor metabolites needed to synthesize nucleotides, while producing reducing power (NADPH)

Phosphorylation potential  The energy required to phosphorylate one mole of ADP by using physiological concentrations of ADP, Pi, and ATP.

Photon  Quantum a particle of light. 

Photosynthesis  The use of light as a source of energy for growth.

Phototroph  Organism  that  uses  light  as  the source of energy for growth.

Phosphotransferase  An enzyme that transfers a phosphorus- containing group from one compound to another, such as the kinases that transfer phosphate groups to proteins.

Photoautotroph  An organism that gains energy for growth from light (electromagnetic radiation) and uses an inorganic carbon molecule such as carbon dioxide as sole carbon source.

Photoheterotroph  An organism that gains energy for growth from light (electromagnetic radiation) and uses an organic carbon molecule as a carbon source.

Photophosphorylation  In photosynthetic microbes, the phosphorylation of ADP to generate ATP using light as the energy source.

Photosystem  In phototrophs, all of the components of the light- harvesting apparatus.

Piezophile  An organism that grows optimally at pressures exceeding 1 atm (see barophile).

Pilin  The peptide subunit that self- assembles to form a pilus.

Porins  large proteins found in the outer membrane of Gram- negative bacteria. They associate to form transmembrane channels that allow the passive diffusion of specific metabolites such as sugars and amino acids.

Proteorhodopsin  A membrane protein in some bacteria that uses energy from sunlight to pump protons out of the cell, thus creating a proton motive force to drive the production of ATP.

Protist  The informal name for an exceedingly diverse group of mostly unicellular eukaryotes.

Proton motive force (PMF)  The force generated by the electrochemical gradient across a cell membrane that drives protons into the cell and is used to power the generation of ATP.

Protoplasts  spherical cells produced experimentally by treating Gram- positive bacteria with lysozyme.

Prototroph  An organism that can make all the metabolic building blocks from precursor metabolites.

Protozoa  The informal name for a group of protists that exhibit animal-like properties such as motility and predation.

Psychrophile  Organism that grows best at temperatures  of  15°C  or  lower,  and  does  not grow above 20°C.

Purple bacteria  A group of anoxygenic phototrophs that contain carotenoid pigments.

Reaction coupling  A tactic for driving essential but unfavorable chemical reactions by coupling them to energetically favorable reactions via energy transfer in the form of high- energy bonds.

Redox potential  The affinity of a molecule for electrons. The more electropositive the potential, the greater the tendency to acquire electrons and thereby be reduced.

Redox reaction  An oxidation- reduction reaction in which one molecule is oxidized (loses electrons) and another is reduced (gains electrons).

Reducing power  A source of electrons (e.g., reduced coenzymes such as NADH and NADPH) used, for example, to make the more reduced building blocks from precursor metabolites.

RuBisCO (ribulose bisphosphate carboxylase)  The key enzyme in carbon dioxide fixation and a constituent of bacterial carboxysomes.

Secondary metabolites  Organic compounds made by organisms which are not directly involved in the growth or reproduction of that organism.

Siderophore  A small molecule secreted by microbes that has exceptionally high affinity for iron and that assists with import of iron into the cell.

Simple diffusion  The basic mechanism of passive transport of solutes across  a membrane without any increase in speed or specificity due to membrane components.

Slime layer  A diffuse layer of secreted exopolysaccharide that is loosely attached to the cell but serves to attach the cell to a surface or provide the matrix for a biofilm.

Spheroplasts  spherical cells produced experimentally by treating Gram- negative bacteria, e.g., with lysozyme.

Spore  A metabolically inert structure formed by some bacteria and fungi in response to adverse conditions and capable of long- term survival  under  those conditions.  

Spore germination  The conversion of a dormant spore into a metabolically active vegetative cell.

Sporulation  The differentiation of a cell into a dormant spore.

Stationary phase  A growth phase in which the rate of cell growth matches the rate of cell death and therefore  there is no change in cell  number.

Strict anaerobes  Organisms that will grow only in the absence of oxygen and are killed by traces of oxygen.

Substrate-level phosphorylation  A process that generates ATP by transferring a high- energy phosphoryl bond from an oxidized metabolic substrate to ADP.

Swarming  A type of flagellar motility exhibited by “rafts” of cells of some types of bacteria on solid surfaces.

Symbiosis  Intimate interaction between two organisms of dif fer ent species, usually with benefits to both partners.

Tautomerism  Refers  to  an  isomerization  in which the isomeric forms are easily interconvertible and an equilibrium exists between the  isomers.  An  example  is  the  enol–keto tautomerization in which enol pyruvic acid readily converts to pyruvic acid.

TCA cycle  A fueling pathway that converts acetyl- coenzyme A (derived from the pyruvate produced by glycolysis) to carbon dioxide, and yields both reducing power and four of the precursor metabolites used in the synthesis of fatty acids and amino acids.

Teichoic acids  Chains of glycerol phosphate or ribitol phosphate linked by phosphodiester bonds and bound covalently to the murein cell wall of Gram- positive bacteria.

Thermoacidophile  A thermophile that is also an acidophile.

Thermophile  An organism that typically grows optimally between 60°C and 85°C.

Thioredoxin  A class of small proteins that are maintained in a reduced state and then function as cellular antioxidants by reducing other compounds.

Thylakoid  Membranous internal compartments in cyanobacteria and chloroplasts whose membrane topology provides increased surface area for the photosynthetic machinery without compromising the exchange of molecules with the cytoplasm.

Transmembrane ion gradient  The electrical potential across a membrane due to a difference in chemical concentration. In cells, typically protons are exported across the membrane and the resultant difference in their concentration generates the proton motive force used to drive ATP production.

Turbidity  The cloudiness of a liquid due to the presence of small, invisible particles such as cells. Measurement of culture turbidity as absorbance or optical density instantly assays the bacterial biomass present (weight/culture volume).

Twitching motility  A type of microbial motility across a surface in which a pilus is extended, its tip adheres to the surface ahead, and then the pilus is retracted to draw the cell forward.

Vesicle  A membrane- bounded structure in the cytoplasm that may be filled with a variety of materials for different purposes, e.g., with gas for buoyancy, with nitrate for a reserve supply.

Viable count  The number of cells in a sample that are capable of reproducing and forming a visible colony in culture, in contrast to the total number of cells present.